David Cameron said he was "profoundly sorry" for the failures that caused the Hillsborough disaster and the subsequent attempts to shift blame for the tragedy on to supporters after the publication of a damning report on the events 23 years ago that left 96 dead.

Speaking in the Commons on Wednesday, the prime minister said the findings in the report were "deeply distressing". He said: "With the weight of the new evidence in the report it's right for me today as prime minister to make a proper apology to the families of the 96 … On behalf of the government, and indeed of our country, I am profoundly sorry that this double injustice has been left uncorrected for so long."

The report by the Hillsborough independent panel, established three years ago and chaired by the bishop of Liverpool, James Jones, found that there was a failure of authorities to protect people and an attempt to blame fans.

The panel concluded that the main cause of the Hillsborough disaster was a "failure in police control" but also revealed "multiple failures" within other organisations that compromised crowd safety. It underlined the "clear operational failure" that led to the disaster and the attempts by South Yorkshire police (SYP) and the ambulance service to cover up their shortcomings. The fact that the ambulance service also altered statements from staff is revealed for the first time. The evidence shows "conclusively" that Liverpool fans "neither caused nor contributed to the deaths" and shows the extent to which attempts, endorsed by the South Yorkshire chief constable Peter Wright, were made to smear them.

Documents released to the panel show how high-ranking police sources, the South Yorkshire Police Federation and the Tory MP Irvine Patnick were responsible for feeding the stories to Whites News Agency in Yorkshire.

They led to the infamous Sun headline "The Truth" that led to a longstanding boycott of the paper in Liverpool.

"The Police Federation, supported informally by the SYP chief constable, sought to develop and publicise a version of events derived in police officers' allegations of drunkenness, ticketless fans and violence. This extended beyond the media to parliament," said the panel."From the mass of documents, television and CCTV coverage disclosed to the panel there is no evidence to support these allegations other than a few isolated examples of aggressive or verbally abusive behaviour clearly reflecting frustration and desperation. The vast majority of fans on the pitch assisted in rescuing and evacuating the dead and injured."

The panel found that 164 police statements were significantly amended and 116 explicitly removed negative comments about the policing operation, including its lack of leadership, a revelation that drew gasps when relayed by Cameron in parliament. Officers carried out police national computer checks on those who had died in an attempt "to impugn the reputations of the deceased" and the coroner took blood alcohol levels from all of the deceased, including children. The panel found that close analysis of the documents demonstrated that the weight placed on blood alcohol levels was inappropriate, fuelling "persistent and unsustainable assertions about drunken fan behaviour not supported by evidence of moderate patterns of drinking unremarkable for a leisure event."

Documents disclosed to the panel also reveal that the original pathologists' evidence of a single unvarying pattern of death is unsustainable. The assumption was the basis of a coroner's imposition of a 3.15pm cut-off on evidence to the inquests. It led to the mistaken belief that an effective emergency service intervention could not have saved lives. The panel's disclosure confirms that in some cases death was not immediate and the outcome depended on events after 3.15pm.

Dr Bill Kirkup, from the panel, said at a press conference at the Anglican cathedral in Liverpool that 41 of the victims had "potential to survive", although he could not say for sure how many could have been saved.

Cameron said it would be for the attorney general to decide whether to apply to the high court to quash the original inquest and seek a new one, as the families are demanding. But he added that it was clear "today's report raises vital questions which must be examined".

The Labour leader, Ed Miliband, made his own apology for his party not doing more to uncover the truth during its 13 years in office from 1997 to 2010. "We on this side also apologise to the families that we didn't do enough to help," he said. A succession of MPs called for legal action against those responsible for the failures that led to the tragedy or who were involved in the subsequent cover-up, variously suggesting that proceedings should be brought for defamation, misconduct in public office and perverting the course of justice.

More than 23 years after 96 men, women and children died in the Leppings Lane end of the ground on 15 April 1989, the families of those who died gave the panel a standing ovation in Liverpool Cathedral as it delivered its findings. "For nearly a quarter of a century the families of the 96 and the survivors of Hillsborough have nursed an open wound waiting for answers to unresolved questions. It has been a frustrating and painful experience adding to their grief. In spite of all the investigations they have sensed that their search for truth and justice has been thwarted and that no one has been held accountable," said Jones. "The documents disclosed to and analysed by the panel show that the tragedy should never have happened. There were clear operational failures in response to the disaster and in its aftermath there were strenuous attempts to deflect the blame on to the fans. The panel's detailed report shows how vulnerable victims, survivors and their families are when transparency and accountability are compromised."

Sheila Coleman of the Hillsborough Justice Campaign welcomed Cameron's apology. She told BBC Radio 4's World at One that the inquest verdicts "have to be quashed" and that criminal charges should be brought "because all the evidence today shows that South Yorkshire police and people in South Yorkshire police lied and operated a cover-up."